To track my time I use an app called Hours Tracker Pro on my iPad (it has a Piggy bank icon) and it allows me to set a rate per client/deal and track time across multiple projects/clients. I also had my contractors use the tool and send me the excel file export from it as you can email the time report to anyone. This let me get their time, take the excel files and create my invoices in my accounting application. It did take an extra step and could have been better, but it wasn't a huge ordeal.
Then for invoicing and getting paid, I used Wave Accounting (but honestly was moving away from it). At least for now, I use Quickbooks for everything Wave used to do for me. Wave has come out with some new features to solve some of the issues I had and to make time tracking etc easier.